Tutorial: Genome Assembly Service

Overview

This set of short videos provides a step-by-step demonstration of using the PATRIC Genome Assembly Service to create an assembled genome from a set a bacterial sequence reads. From these videos you will learn how to do the following:

  • Upload your read files to the private workspace

  • Select assembly strategies and and initiate a Genome Assembly Service job

  • Access and interpret the results from the assembly job

  • Get help if you have problems using the service

Using the Genome Assembly Service

Links to the videos are provided below. They can also be viewed in order in the PATRIC YouTube channel playlist. Relevant references are provided at the bottom of this page.

1. Uploading read files to the workspace (11:08)

2. Submitting reads to the Genome Assembly Service (9:15)

3. Selecting assembly strategies and submitting the assembly job (7:14)

4. Monitoring the assembly jobe and reviewing job results (8:06)

5. Assembly questions and getting help with problems (4:16)

References

  • Antipov, D., et al., plasmidSPAdes: assembling plasmids from whole genome sequencing data. bioRxiv, 2016: p. 048942.

  • Bankevich, A., et al., SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of computational biology, 2012. 19(5): p. 455-477.

  • Gurevich, A., et al., QUAST: quality assessment tool for genome assemblies. Bioinformatics, 2013. 29(8): p. 1072-1075.

  • Koren, S., et al., Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome research, 2017. 27(5): p. 722-736.

  • Krueger, F., Trim Galore: a wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. URL http://www. bioinformatics. babraham. ac. uk/projects/trim_galore/.(Date of access: 28/04/2016), 2012.

  • Nurk, S., et al., metaSPAdes: a new versatile metagenomic assembler. Genome research, 2017. 27(5): p. 824-834.

  • Vaser, R., et al., Fast and accurate de novo genome assembly from long uncorrected reads. Genome research, 2017. 27(5): p. 737-746.

  • Walker, B.J., et al., Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PloS one, 2014. 9(11): p. e112963.

  • Wick, R.R., et al., Bandage: interactive visualization of de novo genome assemblies. Bioinformatics, 2015. 31(20): p. 3350-3352.

  • Wick, R.R., et al., Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS computational biology, 2017. 13(6): p. e1005595.